The Problem & Our Solution

Biology's vast complexity has created a fragmented ecosystem of specialized tools, libraries, websites, and databases. Based on our team's experience, researchers often find themselves juggling 10-15 of these different resources for a single project, manually copying data between them. It’s a massive time-sink that gets in the way of real scientific discovery.

We built Holy Bio MCP to fix this. The impact is a simple but dramatic shift in the research workflow:

• Before: Researchers spend 60-80% of their time on manual data wrangling across a dozen different resources.
• After: A single, conversational command executes the entire workflow: "Find longevity genes → get their 3D structures → find drugs that target them → analyze their interactions."

This is made possible through several concrete applications:

• Interactive Research: Ask complex, multi-step questions in plain English within a chat client and get back synthesized answers.
• AI-Enhanced Development: Supercharge your IDE (like Cursor) with direct, in-editor access to our entire suite of bioinformatics tools.
• Automated Agentic Workflows: Use the framework as a foundational building block for autonomous research agents in platforms like ElizaOS or AutoGen.

To enable this, we developed Holy Bio MCP. The framework was born during the Bio x AI Hackathon from our practical experience building LLM agents at the Longevity Genie project, IBIMA, and the Systems Biology of Aging Group.

What We Built

Our framework consists of two core components: a federation of five specialized servers and a plugin to connect them to the bio.xyz ecosystem.

Holy Bio MCP usage in genetics
Holy Bio MCP usage in longevity and pharmacology

1. A Federation of 5 Specialized MCP Servers

• gget-mcp

  (Genomics Toolkit): For core genomics tasks like BLAST, AlphaFold structure retrieval, and enrichment analysis.

• biothings-mcp

  (Database Hub): Provides unified access to foundational databases like UniProt, PubChem, and ClinVar.

• opengenes-mcp

  (Longevity Genetics): A specialized database to query the genetics of aging and longevity.

• pharmacology-mcp

  (Drug Discovery): Accesses The Guide to PHARMACOLOGY for data on drugs, targets, and ligands.

• synergy-age-mcp

  (Interaction Detective): Uncovers synergistic and antagonistic genetic interactions in longevity.

2. The Biostratum Plugin for ElizaOS

To connect our framework to this hackathon's ecosystem, we also built the Biostratum Plugin. It's a native MCP plugin for ElizaOS designed to integrate our entire server federation with bio.xyz and the broader web3 landscape.